Twain began as a writer of light humorous verse; he ended as a grim, almost profane chronicler of the vanities, hypocrisies and acts of killing committed by mankind. At mid-career, with Huckleberry Finn, he combined rich humor, sturdy narrative and social criticism in a way almost unrivaled in world literature.

Twain was a master at rendering colloquial speech, and helped to create and popularize a distinctive American literature, built on American themes and language.

Twain had a fascination with science and scientific inquiry. Twain developed a close and lasting friendship with Nikola Tesla. They spent quite a bit of time together from time to time (in Tesla's laboratory, among other places). A Connecticut Yankee in King Arthur's Court featured a time traveller from the America of Twain's day who used his knowledge of science to introduce modern technology to Arthurian England.

Twain was a major figure in the Anti-Imperialist League which opposed the annexation of the Philippines by the United States. He wrote "Incident in the Philippines", posthumously published in 1924, in response to the Moro Crater Massacre, in which six hundred Moros were killed.

The name "Mark Twain" is a pun reference to a riverboat depth measurement indicating two fathoms, or "safe water." Some believe that the name "Mark Twain" was brought on by his bad drinking habits, and not by his time as a riverboat pilot. He also used the pseudonym "Sieur Louis de Conte" for his fictional autobiography of Joan of Arc.

In recent years, there have been occasional attempts to ban Huckleberry Finn from various libraries, because Twain's use of local color offends some people. Although Twain was against racism and imperialism far in front of public sentiment of his time, some with only superficial familiarity of his work have condemned it as racist for its accurate depiction of the language in common use in the United States in the 19th century. Expressions that were used casually and unselfconsciously then are often perceived today as racism (in present times, such racial epithets are far more visible and condemned). Twain himself would probably be amused by these attempts; in 1885, when a library in Massachusetts banned the book, he wrote to his publisher, "They have expelled Huck from their library as 'trash suitable only for the slums'. That will sell 25,000 copies for us for sure."

Twain at least saw 1601 published during his lifetime. Twain wrote an anti-war article entitled The War Prayer during the Spanish-American War. It was submitted for publication, but on March 22, 1905, Harper's Bazaar rejected it as "not quite suited to a woman's magazine." Eight days later, Twain wrote to his friend Dan Beard, to whom he had read the story, "I don't think the prayer will be published in my time. None but the dead are permitted to tell the truth." Because he had an exclusive contract with Harper & Brothers, Mark Twain could not publish "The War Prayer" elsewhere and it remained unpublished until 1923.

In his later life Twain's family suppressed some of his work which was especially irreverent towards conventional religion, notably Letters from the Earth, which was not published until 1942.

Perhaps most controversial of all was Mark Twain's 1879 humorous talk at the Stomach Club in Paris entitled Some Thoughts on the Subject of Onanism (masturbation), which concluded with the thought "If you must gamble your lives sexually, don't play a lone hand too much." This talk was not published until 1943, and then only in a limited edition of fifty copies.

Twain's fortunes then began to decline; in his later life, Twain was a very depressed man, but still capable. Twain was able to respond "The report of my death is an exaggeration" in the New York Journal, June 2nd1897. He lost 3 out of 4 of his children, and his beloved wife, Olivia Langdon, before his death in 1910. He also had some very bad times with his businesses. His publishing company ended up going bankrupt, and he lost thousands of dollars on one typesetting machine that was never finished. He also lost a great deal of revenue on royalties from his books being plagiarized before he even had a chance to publish them himself.